The city of San Diego is involved in a legal dispute with a nonprofit church that was hired by police to mentor children at risk of joining gangs.

The dispute involves $43,000 the Metro United Methodist Urban Ministry claims it is owed by San Diego police, who first hired the church to work with vulnerable kids in 2007.

The department used a state grant to pay Metro United $5,000 a month for consulting services until December 2012, when police requested payroll and other records they had not previously sought, the complaint says.

“All of a sudden, the city says we need documentation,” attorney Peter Polischuk said. “We’ve been absolutely pulling our hair out trying to figure out what’s going on.”

Metro United filed suit in July. The city filed a cross-complaint in February, seeking more than $17,000 it claims police wrongly paid to the church, which refuses to return the money.

The police department has had other problems with grant administration of late. The department submitted reports on seized assets to the U.S. Departments of Justice and Treasury with six-figure errors. After U-T Watchdog reported the discrepancies in those filings earlier this month, the department announced it would amend years’ worth of federal records to correct the mistakes.

City attorneys say there is no bookkeeping problem within the San Diego Police Department.

“This case is not about the San Diego Police Department’s accounting practices,” Chief Deputy City Attorney Michael Giorgino said. “The city is defending this matter because plaintiff Metro United Methodist Urban Ministry is suing the city for an alleged breach that occurred over two years after its contract with the city expired. We are defending the city because that is what our job is as the city’s lawyers and our client, the city, denies the validity of this claim.”

Giorgino declined to say how police officials came to overpay the church by more than $17,000.

The litigation is scheduled to go to trial in August.

According to Polischuk, the deputy attorney handling the case, Stacy Plotkin-Wolff, threatened to alert the U.S. Department of Labor to United Metro’s record-keeping problems following a case-management conference March 28. The federal agency recently awarded the church a $9 million contract.

Plotkin-Wolff responded the same day with a one-page letter stating that Polischuk had clearly misconstrued the conversation.

“It appears that you have a suspicious and mistrustful character,” she wrote back. “Please do not transfer your character traits upon me or my client.”

Also in her March 28 letter, Plotkin-Wolff references a suggestion she made earlier that day for both sides to “walk away” from their claims and end the litigation.

Polischuk said that is no longer an option.

“My client is a nonprofit and needs the money, and we think we’ve been mistreated,” he said.

Polischuk said he already held two depositions and is planning four more ahead of the trial. He said he is litigating the case at a discounted rate for the charity because he is bothered by the city’s actions.